Converted template handler to use atomcontainerset

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Dec 8, 2011 · f0cf950 · f0cf950
1 parent 04cbb29
commit f0cf950
Showing 1 changed file with 18 additions and 19 deletions.
diff --git a/src/main/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java b/src/main/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java
@@ -23,28 +23,15 @@
  */
 package org.openscience.cdk.modeling.builder3d;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.zip.GZIPInputStream;
-
-import javax.vecmath.Point3d;
-
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.fingerprint.FingerprinterTool;
 import org.openscience.cdk.fingerprint.HybridizationFingerprinter;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.interfaces.IAtomContainerSet;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.interfaces.IRingSet;
 import org.openscience.cdk.io.iterator.IteratingMDLReader;
 import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
@@ -55,6 +42,18 @@
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.RingSetManipulator;
 
+import javax.vecmath.Point3d;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.zip.GZIPInputStream;
+
 /**
  * Helper class for ModelBuilder3D. Handles templates. This is
  * our layout solution for 3D ring systems
@@ -74,14 +73,14 @@ public class TemplateHandler3D {
 
     IMolecule molecule;
     IRingSet sssr;
-    IMoleculeSet templates = null;
+    IAtomContainerSet templates = null;
     List<BitSet> fingerprintData = null;
     private boolean templatesLoaded = false;
 
     private static TemplateHandler3D self = null;
 
     private TemplateHandler3D() {
-        templates = builder.newInstance(IMoleculeSet.class);
+        templates = builder.newInstance(IAtomContainerSet.class);
         fingerprintData = new ArrayList<BitSet>();
     }
 
@@ -204,7 +203,7 @@ public void mapTemplates(IAtomContainer ringSystems, double NumberOfRingAtoms) t
         boolean flagMaxSubstructure = false;
         boolean flagSecondbest=false;
         for (int i = 0; i < fingerprintData.size(); i++) {
-            IAtomContainer template = templates.getMolecule(i);
+            IAtomContainer template = templates.getAtomContainer(i);
             //if the atom count is different, it can't be right anyway
             if (template.getAtomCount() != ringSystems.getAtomCount()) {
                 continue;
@@ -270,7 +269,7 @@ public int getTemplateCount() {
      *@return The templateAt value
      */
     public IAtomContainer getTemplateAt(int position) {
-        return templates.getMolecule(position);
+        return templates.getAtomContainer(position);
 	}
 }